suppressMessages(library(ArchR))
library(parallel)
library(rhdf5)
library(SingleCellExperiment)
library(SeuratDisk)
library(Seurat)
library(cowplot)
library(here)
ss <- function(x, pattern, slot = 1, ...) { sapply(strsplit(x = x, split = pattern, ...), '[', slot) }
options(stringsAsFactors = F)
options(repr.plot.width=11, repr.plot.height=8.5)
Registered S3 method overwritten by 'SeuratDisk':
method from
as.sparse.H5Group Seurat
Attaching SeuratObject
Attaching package: ‘Seurat’
The following object is masked from ‘package:SummarizedExperiment’:
Assays
here() starts at /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq
Attaching package: ‘here’
The following object is masked from ‘package:plyr’:
here
##################################
### set Arrow File parameters ####
addArchRThreads(threads = round(parallel::detectCores()*1/4))
#addArchRThreads(threads = 1)
##################################
### load rheMac10 ArchR genome ###
# GENOMEDIR='/home/bnphan/resources/genomes/rheMac10'
# load(file.path(GENOMEDIR,'rheMac10_liftoff_GRCh38.p13_ArchR_annotations.rda'))
addArchRGenome("mm10")
Setting default number of Parallel threads to 2. Setting default genome to Mm10.
#correct neuron ArchRProject
PROJDIR='../../../data/tidy_data/ArchRProjects'
ARCHDIR=file.path(PROJDIR,'Mouse_scATAC_DorsalHorn_neuron2')
proj = loadArchRProject(ARCHDIR)
proj
#this project and *_neuron3 are unfinal
ARCHDIR=file.path(PROJDIR,'Mouse_scATAC_DorsalHorn_neuron')
proj2 = loadArchRProject(ARCHDIR)
proj2
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
class: ArchRProject outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_scATAC_DorsalHorn_neuron2 samples(12): Mouse_DH_SEA2253A60 Mouse_DH_SEA2253A61 ... Mouse_DH_SEA2253A69 Mouse_DH_SEA2253A68 sampleColData names(8): ArrowFiles Sample_ID ... Species Region cellColData names(39): Sample TSSEnrichment ... predictedGroup_RNA2ATAC_clustertype predictedScore_RNA2ATAC_clustertype numberOfCells(1): 20591 medianTSS(1): 20.626 medianFrags(1): 25740
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
class: ArchRProject outputDirectory: /projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/ArchRProjects/Mouse_scATAC_DorsalHorn_neuron samples(12): Mouse_DH_SEA2253A61 Mouse_DH_SEA2253A60 ... Mouse_DH_SEA2253A68 Mouse_DH_SEA2253A64 sampleColData names(8): ArrowFiles Sample_ID ... Species Region cellColData names(31): Sample TSSEnrichment ... predictedScore_RNA2ATACCo ClustersX20 numberOfCells(1): 39059 medianTSS(1): 18.496 medianFrags(1): 30306
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersX10", embedding = "UMAPX10")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "predictedGroup_RNA2ATACCo_cell", embedding = "UMAPX10")
ggAlignPlots(p1, p2, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a1e57ce717e2-Date-2023-01-31_Time-19-00-02.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a1e57ce717e2-Date-2023-01-31_Time-19-00-02.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a1e5699a26e6-Date-2023-01-31_Time-19-00-46.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a1e5699a26e6-Date-2023-01-31_Time-19-00-46.log
p1 <- plotEmbedding(ArchRProj = proj2, colorBy = "cellColData",
name = "ClustersX20", embedding = "UMAPX20")
p2 <- plotEmbedding(ArchRProj = proj2, colorBy = "cellColData",
name = "predictedGroup_RNA2ATACCo", embedding = "UMAPX20")
ggAlignPlots(p1, p2, type = "h")
proj <- addImputeWeights(proj, reducedDims = "HarmonyX10")
# proj <- addImputeWeights(proj, reducedDims = "HarmonyX20")
head(getCellColData(proj))
class(getCellColData(proj))
DataFrame with 6 rows and 39 columns
Sample TSSEnrichment
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58 14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58 15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58 10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58 17.269
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse_DH_SEA2253A58 18.201
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT Mouse_DH_SEA2253A58 13.550
ReadsInTSS ReadsInPromoter
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 6788 24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 6990 25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 4355 16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 7718 27008
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 7445 25859
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT 6268 22342
ReadsInBlacklist PromoterRatio PassQC
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 3777 0.155608 1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 3880 0.176551 1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 3561 0.115299 1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 4147 0.185642 1
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 5408 0.183335 1
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT 2593 0.162353 1
NucleosomeRatio nMultiFrags nMonoFrags
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.919877 6002 41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 1.359279 8719 31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 1.350735 7665 31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.868773 4609 38925
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.883453 5368 37444
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT 0.704367 6233 40371
nFrags nDiFrags DoubletScore
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 80176 32413 0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 73534 33647 0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 73444 34536 0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 72742 29208 0
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 70524 27712 0
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT 68807 22203 0
DoubletEnrichment BlacklistRatio
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.3000000 0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.0666667 0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.2666667 0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.4000000 0.0285049
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.5666667 0.0383416
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT 0.3833333 0.0188426
Sample_ID Date.nuclei.prep
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT SEA2253A58 2022-02-15
Biological.rep Age Sex
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT Mouse01-10 0.134247 F/M pool
Species Region ClustersI200
<character> <character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse DorsalHorn C9
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT Mouse DorsalHorn C11
ClustersH200 logNFrags Celltype1
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C14 4.90404 EXC
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C11 4.86649 EXC
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C11 4.86596 EXC
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C11 4.86179 EXC
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC C11 4.84834 EXC
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT C14 4.83763 EXC
ClustersX60 predictedCell_Co
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C6 564
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C9 2290
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C12 2
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C10 4496
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC C16 1570
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT C6 1394
predictedGroup_RNA2ATACCo
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Inh-Cdh3
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVent
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Inh-Rorb
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT Ex-Sox5
predictedScore_RNA2ATACCo ClustersX20
<numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.893739 C4
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.805882 C16
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.931563 C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.564452 C1
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.537839 C13
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT 0.721488 C4
ClustersX10 predictedCell_Co_cell
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C24 564
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C6 2290
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C15 2
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C18 4496
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC C17 1570
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT C24 1394
predictedGroup_RNA2ATACCo_cell
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC GABA4
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT GLUT6
predictedScore_RNA2ATACCo_cell
<numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.893739
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.805882
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.931563
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.564452
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.413136
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT 0.340210
Neuron_Type predictedCell_clustertype
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVent 877
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVent 2290
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA? 1303
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVent 8064
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC GABA2_1, 4_1 4865
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT GLUT3,4,5,6 564
predictedGroup_RNA2ATAC_clustertype
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC midVen
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT midVen
predictedScore_RNA2ATAC_clustertype
<numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 1.000000
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.948107
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.850651
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.408128
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.475185
Mouse_DH_SEA2253A58#GGGTTGCTGCGACTAT 0.361142
# make UMAP plots of
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersX20", embedding = "UMAPX20")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "DoubletEnrichment", embedding = "UMAPX20")
ggAlignPlots(p1, p2, type = "h")
proj$logNFrags = log10(proj$nFrags)
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "logNFrags", embedding = "UMAPX20")
p4 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "TSSEnrichment", embedding = "UMAPX20")
ggAlignPlots(p1, p3, type = "h")
ggAlignPlots(p1, p4, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-336423e32831d-Date-2022-10-11_Time-10-45-11.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-336423e32831d-Date-2022-10-11_Time-10-45-11.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-33642392c94e2-Date-2022-10-11_Time-10-45-28.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-33642392c94e2-Date-2022-10-11_Time-10-45-28.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-33642690a9156-Date-2022-10-11_Time-10-45-36.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-33642690a9156-Date-2022-10-11_Time-10-45-36.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-33642d72462b-Date-2022-10-11_Time-10-45-39.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-33642d72462b-Date-2022-10-11_Time-10-45-39.log
p1 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "ClustersX10", embedding = "UMAPX10")
p2 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "DoubletEnrichment", embedding = "UMAPX10")
ggAlignPlots(p1, p2, type = "h")
proj$logNFrags = log10(proj$nFrags)
p3 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "logNFrags", embedding = "UMAPX10")
p4 <- plotEmbedding(ArchRProj = proj, colorBy = "cellColData",
name = "TSSEnrichment", embedding = "UMAPX10")
ggAlignPlots(p1, p3, type = "h")
ggAlignPlots(p1, p4, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-3364277d82ea4-Date-2022-10-11_Time-10-45-49.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-3364277d82ea4-Date-2022-10-11_Time-10-45-49.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-3364241088620-Date-2022-10-11_Time-10-45-51.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-3364241088620-Date-2022-10-11_Time-10-45-51.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-3364233d8eee7-Date-2022-10-11_Time-10-45-56.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-3364233d8eee7-Date-2022-10-11_Time-10-45-56.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-3364258713911-Date-2022-10-11_Time-10-45-57.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-3364258713911-Date-2022-10-11_Time-10-45-57.log
##########################
# library(SingleCellExperiment)
# library(SeuratDisk)
neuron_data_sce = readRDS("/projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/rdas/macaque_integrated_neuronsv3.mouseGenes.sce.rds")
# neuron_data_sce = LoadH5Seurat("/projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/mmData.comp.adult.2fixerr.h5seurat",assays = "RNA")
# mmSeuratSr <- LoadH5Seurat(mmSeuratFn,assays = "RNA")
# neuron_data_sce[[]][1:5,]
# neuron_data_sce$RNA[1:5,1:5]
# index <- sce$cluster_type != "midVen"
# neuron_data_sce <- sce[,index]
# counts actually natural logcounts, undo first, use `counts` as RNA thing to co-cluster
# counts(neuron_data_sce) = 2.718 ^ logcounts(neuron_data_sce) - 1
#logcounts(neuron_data_sce) = NULL # so only 1 assay available
# has cluster_type data
table(neuron_data_sce$cluster_type)
GLUT1 GLUT2 GLUT3 GLUT4 GLUT5 GLUT6 GLUT7 GLUT8 GLUT9 GLUT10
142 222 152 49 105 123 124 76 98 62
GLUT11 GABA1 GABA2_1 GABA2_2 GABA3 GABA4_1 GABA4_2 GABA5 midVen
89 109 65 71 74 91 100 202 744
head(colData(neuron_data_sce))
table(colData(neuron_data_sce)$cell_type)
table(colData(neuron_data_sce)$cluster_type)
DataFrame with 6 rows and 23 columns
Barcode Unnamed..0
<factor> <integer>
1 AAACCCAAGGATACGC 1
2 AAACCCAAGTAGGTTA 2
4 AAACGAAAGGTGATAT 4
5 AAACGAAGTACCAATC 5
7 AAACGAAGTCCTACGG 7
8 AAACGAAGTTGGGATG 8
Sample
<factor>
1 /projects/pfenninggroup/machineLearningForComputationalBiology/SingleCell/dorsal_horn/P0/Solo.out/
2 /projects/pfenninggroup/machineLearningForComputationalBiology/SingleCell/dorsal_horn/P0/Solo.out/
4 /projects/pfenninggroup/machineLearningForComputationalBiology/SingleCell/dorsal_horn/P0/Solo.out/
5 /projects/pfenninggroup/machineLearningForComputationalBiology/SingleCell/dorsal_horn/P0/Solo.out/
7 /projects/pfenninggroup/machineLearningForComputationalBiology/SingleCell/dorsal_horn/P0/Solo.out/
8 /projects/pfenninggroup/machineLearningForComputationalBiology/SingleCell/dorsal_horn/P0/Solo.out/
cxds_score bcds_score hybrid_score precluster nUMI nGene
<numeric> <numeric> <numeric> <integer> <integer> <integer>
1 151403 0.1023747 0.258838 8 16448 5536
2 207183 0.0779373 0.303326 2 25551 7119
4 126729 0.0457364 0.165572 11 19303 6062
5 345115 0.3334055 0.757984 9 21247 6543
7 224653 0.2941971 0.561554 2 24462 7545
8 180312 0.0766830 0.267683 2 19649 6363
sample_short unique_id precluster_sample size_factor leiden
<factor> <character> <factor> <numeric> <factor>
1 P0 AAACCCAAGGATACGC_P0 8_P0 3.71738 10
2 P0 AAACCCAAGTAGGTTA_P0 2_P0 5.91423 11
4 P0 AAACGAAAGGTGATAT_P0 11_P0 4.29774 3
5 P0 AAACGAAGTACCAATC_P0 9_P0 5.00223 7
7 P0 AAACGAAGTCCTACGG_P0 2_P0 6.25127 0
8 P0 AAACGAAGTTGGGATG_P0 2_P0 4.71166 0
clust_2 cell_type cluster_type mouse_class pred_mm_class_label mouse_family
<factor> <factor> <factor> <factor> <factor> <factor>
1 28 GLUT6 GLUT6 dorsal_excit dorsal_excit Ex-Sox5
2 6 GABA1 GABA1 dorsal_inhib dorsal_inhib Inh-Cdh3
4 26 GABA5 GABA5 dorsal_inhib midVent Inh-Pdyn
5 11 GLUT1 GLUT1 dorsal_excit midVent Ex-Reln
7 21 midVen midVen midVent midVent midVent
8 20 midVen midVen midVent midVent midVent
nCount_RNA nFeature_RNA ident
<numeric> <integer> <factor>
1 20261 16692 AnnData
2 20052 16692 AnnData
4 19517 16692 AnnData
5 19602 16692 AnnData
7 18977 16692 AnnData
8 19448 16692 AnnData
GLUT1 GLUT2 GLUT3 GLUT4 GLUT5 GLUT6 GLUT7 GLUT8 GLUT9 GLUT10 GLUT11 142 222 152 49 105 123 124 76 98 62 89 GABA1 GABA2 GABA3 GABA4 GABA5 midVen 109 136 74 191 202 744
GLUT1 GLUT2 GLUT3 GLUT4 GLUT5 GLUT6 GLUT7 GLUT8 GLUT9 GLUT10
142 222 152 49 105 123 124 76 98 62
GLUT11 GABA1 GABA2_1 GABA2_2 GABA3 GABA4_1 GABA4_2 GABA5 midVen
89 109 65 71 74 91 100 202 744
#####################################
# integration split by tissue region ##Vijay: These are the mouse gene families from the Levine paper I assume
proj = addGeneIntegrationMatrix(
ArchRProj = proj,
useMatrix = "GeneScoreMatrix",
matrixName = "GeneIntegrationMatrix",
reducedDims = "HarmonyX10",
seRNA = neuron_data_sce, nGenes = 2000,
addToArrow = TRUE, plotUMAP = TRUE,
groupRNA = "mouse_family",
nameCell = "predictedCell_Co",
nameGroup = "predictedGroup_RNA2ATACCo",
nameScore = "predictedScore_RNA2ATACCo",
force = TRUE)
proj = saveArchRProject(ArchRProj = proj)
#####################################
# integration split by tissue region ##Vijay: These are the macaque cell types
proj = addGeneIntegrationMatrix(
ArchRProj = proj,
useMatrix = "GeneScoreMatrix",
matrixName = "GeneIntegrationMatrix1",
reducedDims = "HarmonyX10",
seRNA = neuron_data_sce, nGenes = 2000,
addToArrow = TRUE, plotUMAP = TRUE,
groupRNA = "cell_type",
nameCell = "predictedCell_Co_cell",
nameGroup = "predictedGroup_RNA2ATACCo_cell",
nameScore = "predictedScore_RNA2ATACCo_cell",
force = TRUE)
proj = saveArchRProject(ArchRProj = proj)
ArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-b52c6a56c69a-Date-2022-10-07_Time-15-25-48.log
If there is an issue, please report to github with logFile!
2022-10-07 15:25:49 : Running Seurat's Integration Stuart* et al 2019, 0.003 mins elapsed.
2022-10-07 15:25:50 : Checking ATAC Input, 0.034 mins elapsed.
2022-10-07 15:27:04 : Checking RNA Input, 1.26 mins elapsed.
2022-10-07 15:27:14 : Found 15939 overlapping gene names from gene scores and rna matrix!, 1.42 mins elapsed.
2022-10-07 15:27:14 : Creating Integration Blocks, 1.42 mins elapsed.
2022-10-07 15:27:14 : Prepping Interation Data, 1.421 mins elapsed.
2022-10-07 15:27:17 : Computing Integration in 2 Integration Blocks!, 0 mins elapsed.
2022-10-07 15:27:17 : Block (1 of 2) : Computing Integration, 0 mins elapsed.
2022-10-07 15:27:20 : Block (1 of 2) : Identifying Variable Genes, 0.064 mins elapsed.
2022-10-07 15:27:28 : Block (1 of 2) : Getting GeneScoreMatrix, 0.197 mins elapsed.
2022-10-07 15:29:06 : Block (1 of 2) : Imputing GeneScoreMatrix, 1.826 mins elapsed.
Getting ImputeWeights
2022-10-07 15:30:37 : Block (1 of 2) : Seurat FindTransferAnchors, 3.342 mins elapsed.
2022-10-07 15:31:21 : Block (1 of 2) : Seurat TransferData Cell Group Labels, 4.077 mins elapsed.
2022-10-07 15:31:23 : Block (1 of 2) : Seurat TransferData Cell Names Labels, 4.115 mins elapsed.
2022-10-07 15:31:30 : Block (1 of 2) : Seurat TransferData GeneMatrix, 4.217 mins elapsed.
2022-10-07 15:32:09 : Block (1 of 2) : Saving TransferAnchors Joint CCA, 4.877 mins elapsed.
2022-10-07 15:32:11 : Block (1 of 2) : Transferring Paired RNA to Temp File, 4.899 mins elapsed.
2022-10-07 15:33:19 : Block (1 of 2) : Completed Integration, 6.04 mins elapsed.
2022-10-07 15:33:20 : Block (2 of 2) : Computing Integration, 6.057 mins elapsed.
2022-10-07 15:33:23 : Block (2 of 2) : Identifying Variable Genes, 6.116 mins elapsed.
2022-10-07 15:33:33 : Block (2 of 2) : Getting GeneScoreMatrix, 6.269 mins elapsed.
2022-10-07 15:35:49 : Block (2 of 2) : Imputing GeneScoreMatrix, 8.546 mins elapsed.
Getting ImputeWeights
2022-10-07 15:37:48 : Block (2 of 2) : Seurat FindTransferAnchors, 10.517 mins elapsed.
2022-10-07 15:38:26 : Block (2 of 2) : Seurat TransferData Cell Group Labels, 11.149 mins elapsed.
2022-10-07 15:38:28 : Block (2 of 2) : Seurat TransferData Cell Names Labels, 11.189 mins elapsed.
2022-10-07 15:38:34 : Block (2 of 2) : Seurat TransferData GeneMatrix, 11.297 mins elapsed.
2022-10-07 15:39:14 : Block (2 of 2) : Saving TransferAnchors Joint CCA, 11.96 mins elapsed.
2022-10-07 15:39:15 : Block (2 of 2) : Transferring Paired RNA to Temp File, 11.979 mins elapsed.
2022-10-07 15:40:14 : Block (2 of 2) : Completed Integration, 12.96 mins elapsed.
2022-10-07 15:40:15 : Block (1 of 2) : Plotting Joint UMAP, 12.975 mins elapsed.
WARNING: Error found with Cairo installation. Continuing without rasterization.
WARNING: Error found with Cairo installation. Continuing without rasterization.
2022-10-07 15:40:53 : Block (2 of 2) : Plotting Joint UMAP, 13.601 mins elapsed.
WARNING: Error found with Cairo installation. Continuing without rasterization.
WARNING: Error found with Cairo installation. Continuing without rasterization.
2022-10-07 15:41:29 : Transferring Data to ArrowFiles, 14.202 mins elapsed.
2022-10-07 15:41:29 : Mouse_DH_SEA2253A60 (1 of 12) Getting GeneIntegrationMatrix From TempFiles!, 14.208 mins elapsed.
2022-10-07 15:41:47 : Mouse_DH_SEA2253A60 (1 of 12) Adding GeneIntegrationMatrix to ArrowFile!, 14.51 mins elapsed.
2022-10-07 15:44:00 : Mouse_DH_SEA2253A62 (3 of 12) Getting GeneIntegrationMatrix From TempFiles!, 16.727 mins elapsed.
2022-10-07 15:44:18 : Mouse_DH_SEA2253A62 (3 of 12) Adding GeneIntegrationMatrix to ArrowFile!, 17.024 mins elapsed.
2022-10-07 15:45:32 : Mouse_DH_SEA2253A59 (4 of 12) Getting GeneIntegrationMatrix From TempFiles!, 18.253 mins elapsed.
2022-10-07 15:45:58 : Mouse_DH_SEA2253A59 (4 of 12) Adding GeneIntegrationMatrix to ArrowFile!, 18.687 mins elapsed.
2022-10-07 15:47:04 : Mouse_DH_SEA2253A58 (5 of 12) Getting GeneIntegrationMatrix From TempFiles!, 19.799 mins elapsed.
2022-10-07 15:47:21 : Mouse_DH_SEA2253A58 (5 of 12) Adding GeneIntegrationMatrix to ArrowFile!, 20.072 mins elapsed.
2022-10-07 15:48:08 : Mouse_DH_SEA2253A66 (6 of 12) Getting GeneIntegrationMatrix From TempFiles!, 20.856 mins elapsed.
2022-10-07 15:48:21 : Mouse_DH_SEA2253A66 (6 of 12) Adding GeneIntegrationMatrix to ArrowFile!, 21.068 mins elapsed.
2022-10-07 15:49:02 : Mouse_DH_SEA2253A63 (7 of 12) Getting GeneIntegrationMatrix From TempFiles!, 21.756 mins elapsed.
2022-10-07 15:49:19 : Mouse_DH_SEA2253A63 (7 of 12) Adding GeneIntegrationMatrix to ArrowFile!, 22.049 mins elapsed.
2022-10-07 15:50:12 : Mouse_DH_SEA2253A67 (8 of 12) Getting GeneIntegrationMatrix From TempFiles!, 22.93 mins elapsed.
2022-10-07 15:50:24 : Mouse_DH_SEA2253A67 (8 of 12) Adding GeneIntegrationMatrix to ArrowFile!, 23.125 mins elapsed.
2022-10-07 15:51:09 : Mouse_DH_SEA2253A65 (9 of 12) Getting GeneIntegrationMatrix From TempFiles!, 23.869 mins elapsed.
2022-10-07 15:51:20 : Mouse_DH_SEA2253A65 (9 of 12) Adding GeneIntegrationMatrix to ArrowFile!, 24.051 mins elapsed.
2022-10-07 15:52:06 : Mouse_DH_SEA2253A64 (10 of 12) Getting GeneIntegrationMatrix From TempFiles!, 24.816 mins elapsed.
2022-10-07 15:52:18 : Mouse_DH_SEA2253A64 (10 of 12) Adding GeneIntegrationMatrix to ArrowFile!, 25.026 mins elapsed.
2022-10-07 15:53:03 : Mouse_DH_SEA2253A69 (11 of 12) Getting GeneIntegrationMatrix From TempFiles!, 25.768 mins elapsed.
2022-10-07 15:53:12 : Mouse_DH_SEA2253A69 (11 of 12) Adding GeneIntegrationMatrix to ArrowFile!, 25.925 mins elapsed.
2022-10-07 15:53:58 : Mouse_DH_SEA2253A68 (12 of 12) Getting GeneIntegrationMatrix From TempFiles!, 26.687 mins elapsed.
2022-10-07 15:54:07 : Mouse_DH_SEA2253A68 (12 of 12) Adding GeneIntegrationMatrix to ArrowFile!, 26.849 mins elapsed.
2022-10-07 15:54:59 : Completed Integration with RNA Matrix, 27.708 mins elapsed.
ArchR logging successful to : ArchRLogs/ArchR-addGeneIntegrationMatrix-b52c6a56c69a-Date-2022-10-07_Time-15-25-48.log
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
#####################################
#integration split by tissue region
proj = addGeneIntegrationMatrix(
ArchRProj = proj,
useMatrix = "GeneScoreMatrix",
matrixName = "GeneIntegrationMatrix1",
reducedDims = "HarmonyX10",
seRNA = neuron_data_sce, nGenes = 2000,
addToArrow = TRUE, plotUMAP = TRUE,
groupRNA = "cluster_type",
nameCell = "predictedCell_clustertype",
nameGroup = "predictedGroup_RNA2ATAC_clustertype",
nameScore = "predictedScore_RNA2ATAC_clustertype",
force = TRUE)
# proj = saveArchRProject(ArchRProj = proj)
ArchR logging to : ArchRLogs/ArchR-addGeneIntegrationMatrix-6a1e54ee9c6f2-Date-2023-01-31_Time-19-04-56.log If there is an issue, please report to github with logFile! 2023-01-31 19:04:59 : Running Seurat's Integration Stuart* et al 2019, 0.054 mins elapsed. 2023-01-31 19:05:01 : Checking ATAC Input, 0.092 mins elapsed. 2023-01-31 19:05:51 : Checking RNA Input, 0.919 mins elapsed. 2023-01-31 19:05:57 : Found 15939 overlapping gene names from gene scores and rna matrix!, 1.02 mins elapsed. 2023-01-31 19:05:59 : Creating Integration Blocks, 1.051 mins elapsed. 2023-01-31 19:05:59 : Prepping Interation Data, 1.052 mins elapsed. 2023-01-31 19:06:00 : Computing Integration in 2 Integration Blocks!, 0 mins elapsed. 2023-01-31 19:13:26 : Block (1 of 2) : Plotting Joint UMAP, 7.43 mins elapsed. WARNING: Error found with Cairo installation. Continuing without rasterization. WARNING: Error found with Cairo installation. Continuing without rasterization. 2023-01-31 19:14:04 : Block (2 of 2) : Plotting Joint UMAP, 8.07 mins elapsed. WARNING: Error found with Cairo installation. Continuing without rasterization. WARNING: Error found with Cairo installation. Continuing without rasterization. 2023-01-31 19:14:48 : Transferring Data to ArrowFiles, 8.79 mins elapsed. 2023-01-31 19:27:54 : Completed Integration with RNA Matrix, 21.902 mins elapsed. ArchR logging successful to : ArchRLogs/ArchR-addGeneIntegrationMatrix-6a1e54ee9c6f2-Date-2023-01-31_Time-19-04-56.log
getCellColData(proj)
Error in getCellColData(proj): could not find function "getCellColData" Traceback:
cM <- confusionMatrix(paste0(proj$predictedGroup_RNA2ATACCo), paste0(proj$ClustersX10))
cM <- cM / Matrix::colSums(cM)
cM = cM[,order(colnames(cM))]
p <- pheatmap::pheatmap(
mat = as.matrix(cM),
color = paletteContinuous("whiteBlue"),
border_color = "black")
p
cM <- confusionMatrix(paste0(proj$predictedGroup_RNA2ATACCo_cell), paste0(proj$predictedGroup_RNA2ATAC_clustertype))
cM <- cM / Matrix::colSums(cM)
cM = cM[,order(colnames(cM))]
p <- pheatmap::pheatmap(
mat = as.matrix(cM),
color = paletteContinuous("whiteBlue"),
border_color = "black")
p
p1 <- plotEmbedding( proj, colorBy = "cellColData", name = "predictedGroup_RNA2ATACCo_cell", embedding = "UMAPX10")
p2 <- plotEmbedding( proj, colorBy = "cellColData", name = "predictedGroup_RNA2ATAC_clustertype", embedding = "UMAPX10")
p3 <- plotEmbedding( proj, colorBy = "cellColData", name = "ClustersX10", embedding = "UMAPX10")
ggAlignPlots(p3, p2, p1, type = "h")
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a1e520ed92de-Date-2023-01-31_Time-20-48-41.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a1e520ed92de-Date-2023-01-31_Time-20-48-41.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a1e53409a3dc-Date-2023-01-31_Time-20-49-18.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a1e53409a3dc-Date-2023-01-31_Time-20-49-18.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-6a1e553d05c05-Date-2023-01-31_Time-20-49-24.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-6a1e553d05c05-Date-2023-01-31_Time-20-49-24.log
## Marker Genes for differentiation of Inhibitory Nuerons
markerGenes1 <- c('MASP1', # GABA 1
# 'GDNF-AS1', # GABA 2
'RREB1', # GABA 2
'NPY', # GABA 3
'MET', # GABA 4
'PTN', # GABA 4
'PDYN' # GABA 5
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPX10")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-336422b6c1765-Date-2022-10-11_Time-10-48-45.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-11 10:48:46 : 1 2 3 4 5 6 7 8 9 10 11 12 Imputing Matrix Using weights on disk 1 of 4 2 of 4 3 of 4 4 of 4 Using weights on disk 1 of 4 2 of 4 3 of 4 4 of 4 Plotting Embedding 1 2 3 4 5 6 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-336422b6c1765-Date-2022-10-11_Time-10-48-45.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Marker Genes for differentiation of Excitatory Neurons
markerGenes1 <- c('GFRA1', #GLUT 1,2
# 'TAC3', #GLUT 3,4
'GHR', #GLUT 5,6
'TAC1', #GLUT 6
'ADARB2', #GLUT 7-10
'MAF', #GLUT 7
'ST8SIA6', #GLUT 8
'NTNG1', #GLUT 9,10
'SOX5' #GLUT6,6?
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPX10")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-336425e10ad8c-Date-2022-10-11_Time-10-50-02.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-11 10:50:04 : 1 2 3 4 5 6 7 8 9 10 11 12 Imputing Matrix Using weights on disk 1 of 4 2 of 4 3 of 4 4 of 4 Using weights on disk 1 of 4 2 of 4 3 of 4 4 of 4 Plotting Embedding 1 2 3 4 5 6 7 8 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-336425e10ad8c-Date-2022-10-11_Time-10-50-02.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Marker Genes for differentiation of Excitatory Neurons
markerGenes1 <- c('COL24A1', #GLUT 5
'CRHR2', #GLUT 1
'COL13A1', #GLUT 1
'NMUR2', #GLUT 2
'NMU', #GLUT 3
'COL5A2', #GLUT 4
'NMBR', #GLUT 5
'TAC1' #GLUT 6
# 'ANOS1' #GLUT 6
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPX10")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-336423f0333f-Date-2022-10-11_Time-10-51-22.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-11 10:51:24 : 1 2 3 4 5 6 7 8 9 10 11 12 Imputing Matrix Using weights on disk 1 of 4 2 of 4 3 of 4 4 of 4 Using weights on disk 1 of 4 2 of 4 3 of 4 4 of 4 Plotting Embedding 1 2 3 4 5 6 7 8 ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-336423f0333f-Date-2022-10-11_Time-10-51-22.log Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.” Warning message: “`guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.”
## Marker Genes for differentiation of Excitatory Neurons
markerGenes1 <- c('COL21A1', #GLUT 7
'MAF', #GLUT 7
'MAFA', #GLUT 8
'ADAMTS16', #GLUT 9
'TLL2', #GLUT 9
'OTOGL', #GLUT 10
'PDYN' #GLUT 11
)
p <- plotEmbedding( ArchRProj = proj, colorBy = "GeneScoreMatrix",
name = markerGenes1, embedding = "UMAPX10")
p <- lapply(p, function(x){
x + guides(color = FALSE, fill = FALSE) +
theme_ArchR(baseSize = 6.5) + theme(plot.margin = unit(c(0, 0, 0, 0), "cm")) +
theme( axis.text.x=element_blank(), axis.ticks.x=element_blank(),
axis.text.y=element_blank(), axis.ticks.y=element_blank())
})
do.call(cowplot::plot_grid, c(list(ncol = 3),p))
Getting ImputeWeights ArchR logging to : ArchRLogs/ArchR-plotEmbedding-3364272610c0c-Date-2022-10-11_Time-10-54-36.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = GeneScoreMatrix Getting Matrix Values... 2022-10-11 10:54:37 : FeatureName (COL21A1) does not exist! See getFeatures
Error:
Traceback:
1. plotEmbedding(ArchRProj = proj, colorBy = "GeneScoreMatrix",
. name = markerGenes1, embedding = "UMAPX10")
2. .getMatrixValues(ArchRProj = ArchRProj, name = name, matrixName = colorBy,
. log2Norm = FALSE, threads = threads, logFile = logFile)
3. .logStop(sprintf("FeatureName (%s) does not exist! See getFeatures",
. paste0(name[which(is.na(idx))], collapse = ",")), logFile = logFile)
4. stop(sprintf("%s\n", msg), call. = FALSE)
p1 <- plotEmbedding( proj, colorBy = "cellColData", name = "predictedGroup_RNA2ATAC_clustertype", embedding = "UMAPX10")
p2 <- plotEmbedding( proj, colorBy = "cellColData", name = "predictedGroup_RNA2ATACCo", embedding = "UMAPX10")
p3 <- plotEmbedding( proj, colorBy = "cellColData", name = "predictedGroup_RNA2ATACCo_cell", embedding = "UMAPX10")
p4 <- plotEmbedding( proj, colorBy = "cellColData", name = "ClustersX10", embedding = "UMAPX10")
plot_grid(p1, p2, p3, p4)
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-42341bd3684d-Date-2023-02-15_Time-10-23-58.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-42341bd3684d-Date-2023-02-15_Time-10-23-58.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-42341f695b9d-Date-2023-02-15_Time-10-24-00.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-42341f695b9d-Date-2023-02-15_Time-10-24-00.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-4234150d9f18-Date-2023-02-15_Time-10-24-02.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-4234150d9f18-Date-2023-02-15_Time-10-24-02.log ArchR logging to : ArchRLogs/ArchR-plotEmbedding-42341cc39d43-Date-2023-02-15_Time-10-24-04.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. Length of unique values greater than palette, interpolating.. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-42341cc39d43-Date-2023-02-15_Time-10-24-04.log
#final cluster w/ RNA labels embedding
p3 <- plotEmbedding( proj, colorBy = "cellColData", name = "predictedGroup_RNA2ATAC_clustertype", embedding = "UMAPX10")
p3
ArchR logging to : ArchRLogs/ArchR-plotEmbedding-4234473d20f2-Date-2023-02-15_Time-10-24-17.log If there is an issue, please report to github with logFile! Getting UMAP Embedding ColorBy = cellColData Plotting Embedding 1 WARNING: Error found with Cairo installation. Continuing without rasterization. ArchR logging successful to : ArchRLogs/ArchR-plotEmbedding-4234473d20f2-Date-2023-02-15_Time-10-24-17.log
# drop the UNK cluster
idxSample <- BiocGenerics::which(proj$predictedGroup_RNA2ATACCo %ni% c('Drop'))
table(proj$predictedGroup_RNA2ATACCo[idxSample])
cellsSample <- proj$cellNames[idxSample]
proj = subsetCells(ArchRProj = proj, cellNames = cellsSample)
proj = saveArchRProject(ArchRProj = proj)
#add FINAL LABELS column to all projects
proj <- addCellColData(ArchRProj = proj, data = proj$predictedGroup_RNA2ATAC_clustertype,
cells = rownames(getCellColData(proj)), name = "FINAL_GROUP_LABEL", force = TRUE)
names(getCellColData(proj))
getCellColData(proj)
DataFrame with 20591 rows and 40 columns
Sample TSSEnrichment
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58 14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58 15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58 10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58 17.269
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse_DH_SEA2253A58 18.201
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG Mouse_DH_SEA2253A69 8.303
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG Mouse_DH_SEA2253A69 9.596
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC Mouse_DH_SEA2253A69 50.724
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG Mouse_DH_SEA2253A69 31.498
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT Mouse_DH_SEA2253A69 30.471
ReadsInTSS ReadsInPromoter
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 6788 24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 6990 25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 4355 16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 7718 27008
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 7445 25859
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 348 1581
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 378 1668
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 1332 3902
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 1193 3754
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 754 2477
ReadsInBlacklist PromoterRatio PassQC
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 3777 0.155608 1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 3880 0.176551 1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 3561 0.115299 1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 4147 0.185642 1
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 5408 0.183335 1
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 244 0.117094 1
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 202 0.128052 1
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 340 0.301966 1
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 240 0.302742 1
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 247 0.256365 1
NucleosomeRatio nMultiFrags nMonoFrags
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.919877 6002 41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 1.359279 8719 31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 1.350735 7665 31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.868773 4609 38925
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.883453 5368 37444
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 6.054336 1442 957
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 8.808735 1299 664
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 0.137300 189 5681
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 0.130562 152 5484
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 0.661279 368 2908
nFrags nDiFrags DoubletScore
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 80176 32413 0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 73534 33647 0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 73444 34536 0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 72742 29208 0
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 70524 27712 0
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 6751 4352 0
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 6513 4550 0
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 6461 591 0
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 6200 564 0
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 4831 1555 0
DoubletEnrichment BlacklistRatio
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.3000000 0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.0666667 0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.2666667 0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.4000000 0.0285049
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.5666667 0.0383416
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 1.0222222 0.0180714
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 0.2222222 0.0155074
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 0.0222222 0.0263117
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 0.0000000 0.0193548
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 0.2000000 0.0255641
Sample_ID Date.nuclei.prep
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC SEA2253A58 2022-02-15
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT SEA2253A69 2022-02-23
Biological.rep Age Sex
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse01-10 0.134247 F/M pool
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT Mouse11-20 0.156164 F/M pool
Species Region ClustersI200
<character> <character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse DorsalHorn C9
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG Mouse DorsalHorn C14
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG Mouse DorsalHorn C5
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC Mouse DorsalHorn C15
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG Mouse DorsalHorn C15
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT Mouse DorsalHorn C15
ClustersH200 logNFrags Celltype1
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C14 4.90404 EXC
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C11 4.86649 EXC
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C11 4.86596 EXC
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C11 4.86179 EXC
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC C11 4.84834 EXC
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG C14 3.82937 EXC
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG C7 3.81378 INH
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC C15 3.81030 EXC
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG C15 3.79239 EXC
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT C15 3.68404 EXC
ClustersX60 predictedCell_Co
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C6 564
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C9 2290
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C12 2
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C10 4496
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC C16 1570
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG C22 10242
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG C17 8674
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC C20 8839
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG C20 1590
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT C20 8839
predictedGroup_RNA2ATACCo
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Inh-Cdh3
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVent
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Inh-Rorb
... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG Ex-Sox5
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG Inh-Adamts5
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC Ex-Reln
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG Ex-Reln
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT Ex-Reln
predictedScore_RNA2ATACCo ClustersX20
<numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.893739 C4
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.805882 C16
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.931563 C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.564452 C1
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.537839 C13
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 0.665456 C18
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 0.949357 C14
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 0.819760 C25
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 0.991770 C25
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 0.881383 C25
ClustersX10 predictedCell_Co_cell
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C24 564
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C6 2290
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C15 2
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C18 4496
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC C17 1570
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG C11 10242
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG C13 8674
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC C5 8839
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG C5 1590
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT C5 8839
predictedGroup_RNA2ATACCo_cell
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC GABA4
... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG GLUT4
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG GABA4
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC GLUT2
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG GLUT2
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT GLUT2
predictedScore_RNA2ATACCo_cell
<numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.893739
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.805882
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.931563
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.564452
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.413136
... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 0.551314
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 0.918794
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 0.636967
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 0.909557
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 0.705046
Neuron_Type predictedCell_clustertype
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVent 877
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVent 2290
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA? 1303
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVent 8064
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC GABA2_1, 4_1 4865
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG GLUT3,4,5,6 11604
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG GABA2_2, 4_2 8674
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC GLUT1,2 9196
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG GLUT1,2 1756
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT GLUT1,2 1756
predictedGroup_RNA2ATAC_clustertype
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC midVen
... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG GLUT3
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG GABA4_2
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC GLUT2
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG GLUT2
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT GLUT2
predictedScore_RNA2ATAC_clustertype
<numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 1.000000
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.948107
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.850651
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.408128
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.475185
... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 0.667286
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 0.897909
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 0.892677
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 0.889763
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 0.911827
FINAL_GROUP_LABEL
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC midVen
... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG GLUT3
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG GABA4_2
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC GLUT2
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG GLUT2
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT GLUT2
table(proj$predictedGroup_RNA2ATAC_clustertype)
table(proj$FINAL_GROUP_LABEL)
proj = saveArchRProject(ArchRProj = proj)
GABA1 GABA2_1 GABA2_2 GABA3 GABA4_1 GABA4_2 GABA5 GLUT1 GLUT10 GLUT11 1078 64 1545 376 967 795 1320 1092 431 39 GLUT2 GLUT3 GLUT4 GLUT5 GLUT6 GLUT7 GLUT8 GLUT9 midVen 2452 1945 341 992 2195 2283 1157 1 1518
GABA1 GABA2_1 GABA2_2 GABA3 GABA4_1 GABA4_2 GABA5 GLUT1 GLUT10 GLUT11 1078 64 1545 376 967 795 1320 1092 431 39 GLUT2 GLUT3 GLUT4 GLUT5 GLUT6 GLUT7 GLUT8 GLUT9 midVen 2452 1945 341 992 2195 2283 1157 1 1518
Saving ArchRProject...
Loading ArchRProject...
Successfully loaded ArchRProject!
/ |
/ \
. / |.
\\\ / |.
\\\ / `|.
\\\ / |.
\ / |\
\\#####\ / ||
==###########> / ||
\\##==......\ / ||
______ = =|__ /__ || \\\
,--' ,----`-,__ ___/' --,-`-===================##========>
\ ' ##_______ _____ ,--,__,=##,__ ///
, __== ___,-,__,--'#' ===' `-' | ##,-/
-,____,---' \\####\\________________,--\\_##,/
___ .______ ______ __ __ .______
/ \ | _ \ / || | | | | _ \
/ ^ \ | |_) | | ,----'| |__| | | |_) |
/ /_\ \ | / | | | __ | | /
/ _____ \ | |\ \\___ | `----.| | | | | |\ \\___.
/__/ \__\ | _| `._____| \______||__| |__| | _| `._____|
# MAT <- getMatrixFromProject(
# ArchRProj = proj,
# useMatrix = "GeneScoreMatrix",
# useSeqnames = NULL,
# verbose = TRUE,
# binarize = FALSE,
# threads = getArchRThreads(),
# logFile = createLogFile("getMatrixFromProject")
# )
# ## # plot the confusion matrix of cell types by predicted cell type clusters
# cM <- confusionMatrix(paste0(proj$Neuron_Type), paste0(proj$ClustersX10))
# cM <- cM / Matrix::colSums(cM)
# cM = cM[,order(colnames(cM))]
# p <- pheatmap::pheatmap(
# mat = as.matrix(cM),
# color = paletteContinuous("whiteBlue"),
# border_color = "black")
# p
# preClust <- rownames(cM)[apply(cM, 2 , which.max)]
# cbind(preClust, colnames(cM)) #Assignments
| preClust | |
|---|---|
| GLUT1,2 | C1 |
| GLUT3,4,5,6 | C10 |
| GLUT3,4,5,6 | C11 |
| GABA2_2, 4_2 | C12 |
| GABA2_2, 4_2 | C13 |
| GABA2_1, 4_1 | C14 |
| GABA? | C15 |
| GABA? | C16 |
| GABA2_1, 4_1 | C17 |
| GLUT1,2 | C18 |
| GABA5 | C19 |
| GLUT8 | C2 |
| GABA3 | C20 |
| midVent | C21 |
| GLUT3,4,5,6 | C22 |
| GLUT3,4,5,6 | C23 |
| GLUT3,4,5,6 | C24 |
| GLUT3,4,5,6 | C25 |
| GLUT9,10 | C3 |
| GLUT1,2 | C4 |
| GLUT1,2 | C5 |
| GLUT7,8 | C6 |
| GLUT7,8 | C7 |
| GLUT3,4,5,6 | C8 |
| GLUT7,8 | C9 |
# library(SingleCellExperiment)
# library(SeuratDisk)
# sce = LoadH5Seurat("/projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/mmData.comp.adult.2fixerr.h5seurat",assays = "RNA")
# neuron_data_sce <- as.SingleCellExperiment(sce)
# neuron_data_sce
# counts(neuron_data_sce)
# 2.718 ^ logcounts(neuron_data_sce) - 1
# #manually labelling ATAC clusters, going with RNA integrated labels
# remap = c(
# 'Ex-Cpne4'='GLUT8',
# 'Ex-Maf'='GLUT7,8',
# 'Ex-Prkcg'='GLUT9,10',
# 'Ex-Reln'='GLUT1,2',
# 'Ex-Rreb1'='GLUT11',
# 'Ex-Sox5'='GLUT3,4,5,6',
# 'Inh-Adamts5'='GABA2_2, 4_2',
# 'Inh-Npy'='GABA3',
# 'Inh-Pdyn'='GABA5',
# 'Inh-Rorb'='GABA2_1, 4_1',
# 'Inh-Cdh3' = 'GABA?',
# 'midVent = midVent'
# )
# proj$Neuron_Type = mapLabels(proj$predictedGroup_RNA2ATACCo, newLabels = remap, oldLabels = names(remap))
# getCellColData(proj)
The following `from` values were not present in `x`:
DataFrame with 20591 rows and 36 columns
Sample TSSEnrichment
<character> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse_DH_SEA2253A58 14.164
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse_DH_SEA2253A58 15.910
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse_DH_SEA2253A58 10.861
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse_DH_SEA2253A58 17.269
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse_DH_SEA2253A58 18.201
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG Mouse_DH_SEA2253A69 8.303
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG Mouse_DH_SEA2253A69 9.596
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC Mouse_DH_SEA2253A69 50.724
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG Mouse_DH_SEA2253A69 31.498
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT Mouse_DH_SEA2253A69 30.471
ReadsInTSS ReadsInPromoter
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 6788 24952
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 6990 25965
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 4355 16936
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 7718 27008
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 7445 25859
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 348 1581
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 378 1668
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 1332 3902
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 1193 3754
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 754 2477
ReadsInBlacklist PromoterRatio PassQC
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 3777 0.155608 1
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 3880 0.176551 1
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 3561 0.115299 1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 4147 0.185642 1
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 5408 0.183335 1
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 244 0.117094 1
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 202 0.128052 1
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 340 0.301966 1
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 240 0.302742 1
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 247 0.256365 1
NucleosomeRatio nMultiFrags nMonoFrags
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.919877 6002 41761
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 1.359279 8719 31168
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 1.350735 7665 31243
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.868773 4609 38925
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.883453 5368 37444
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 6.054336 1442 957
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 8.808735 1299 664
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 0.137300 189 5681
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 0.130562 152 5484
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 0.661279 368 2908
nFrags nDiFrags DoubletScore
<numeric> <numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 80176 32413 0
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 73534 33647 0
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 73444 34536 0
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 72742 29208 0
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 70524 27712 0
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 6751 4352 0
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 6513 4550 0
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 6461 591 0
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 6200 564 0
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 4831 1555 0
DoubletEnrichment BlacklistRatio
<numeric> <numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.3000000 0.0235544
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.0666667 0.0263824
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.2666667 0.0242430
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.4000000 0.0285049
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.5666667 0.0383416
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 1.0222222 0.0180714
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 0.2222222 0.0155074
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 0.0222222 0.0263117
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 0.0000000 0.0193548
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 0.2000000 0.0255641
Sample_ID Date.nuclei.prep
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG SEA2253A58 2022-02-15
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC SEA2253A58 2022-02-15
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG SEA2253A69 2022-02-23
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT SEA2253A69 2022-02-23
Biological.rep Age Sex
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse01-10 0.134247 F/M pool
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse01-10 0.134247 F/M pool
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG Mouse11-20 0.156164 F/M pool
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT Mouse11-20 0.156164 F/M pool
Species Region ClustersI200
<character> <character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG Mouse DorsalHorn C11
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Mouse DorsalHorn C9
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG Mouse DorsalHorn C14
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG Mouse DorsalHorn C5
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC Mouse DorsalHorn C15
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG Mouse DorsalHorn C15
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT Mouse DorsalHorn C15
ClustersH200 logNFrags Celltype1
<character> <numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C14 4.90404 EXC
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C11 4.86649 EXC
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C11 4.86596 EXC
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C11 4.86179 EXC
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC C11 4.84834 EXC
... ... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG C14 3.82937 EXC
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG C7 3.81378 INH
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC C15 3.81030 EXC
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG C15 3.79239 EXC
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT C15 3.68404 EXC
ClustersX60 predictedCell_Co
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C6 564
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C9 2290
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C12 2
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C10 4496
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC C16 1570
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG C22 10242
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG C17 8674
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC C20 8839
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG C20 1590
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT C20 8839
predictedGroup_RNA2ATACCo
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG Inh-Cdh3
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVent
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC Inh-Rorb
... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG Ex-Sox5
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG Inh-Adamts5
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC Ex-Reln
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG Ex-Reln
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT Ex-Reln
predictedScore_RNA2ATACCo ClustersX20
<numeric> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.893739 C4
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.805882 C16
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.931563 C11
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.564452 C1
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.537839 C13
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 0.665456 C18
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 0.949357 C14
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 0.819760 C25
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 0.991770 C25
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 0.881383 C25
ClustersX10 predictedCell_Co_cell
<character> <character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA C24 564
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT C6 2290
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG C15 2
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG C18 4496
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC C17 1570
... ... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG C11 10242
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG C13 8674
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC C5 8839
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG C5 1590
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT C5 8839
predictedGroup_RNA2ATACCo_cell
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVen
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVen
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA1
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVen
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC GABA4
... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG GLUT4
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG GABA4
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC GLUT2
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG GLUT2
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT GLUT2
predictedScore_RNA2ATACCo_cell
<numeric>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA 0.893739
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT 0.805882
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG 0.931563
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG 0.564452
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC 0.413136
... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG 0.551314
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG 0.918794
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC 0.636967
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG 0.909557
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT 0.705046
Neuron_Type
<character>
Mouse_DH_SEA2253A58#TTACACACTTCGTCAA midVent
Mouse_DH_SEA2253A58#GCGTGCTGAAGCAGGT midVent
Mouse_DH_SEA2253A58#CGACCAGACTTCTGAG GABA?
Mouse_DH_SEA2253A58#TCAGTCCTGAATACAG midVent
Mouse_DH_SEA2253A58#GCTTTAGGATCGTAAC GABA2_1, 4_1
... ...
Mouse_DH_SEA2253A69#GACCCATCTTAGCAGG GLUT3,4,5,6
Mouse_DH_SEA2253A69#GACAGGAACTTCTGAG GABA2_2, 4_2
Mouse_DH_SEA2253A69#CTACGTGCTAGGTCCC GLUT1,2
Mouse_DH_SEA2253A69#ATGTTTCACGCCGTTG GLUT1,2
Mouse_DH_SEA2253A69#GCGTCGATGGTTGACT GLUT1,2
##########################
# library(SingleCellExperiment)
# library(SeuratDisk)
#sce = LoadH5Seurat("/projects/pfenninggroup/singleCell/Macaque_SealDorsalHorn_snATAC-seq/data/tidy_data/mmData.comp.adult.2fixerr.h5seurat",assays = "RNA")
#neuron_data_sce <- as.SingleCellExperiment(sce)
# counts actually natural logcounts, undo first, use `counts` as RNA thing to co-cluster
# counts(neuron_data_sce) = 2.718 ^ logcounts(neuron_data_sce) - 1
# logcounts(neuron_data_sce) = NULL # so only 1 assay available
#logcounts(neuron_data_sce) = NULL
# has cluster_type data
# table(neuron_data_sce$cluster_type)